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Nature Jan 2020The origin of eukaryotes remains unclear. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea. Despite the...
The origin of eukaryotes remains unclear. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E) model.
Topics: Amino Acids; Archaea; Eukaryotic Cells; Evolution, Molecular; Genome, Archaeal; Geologic Sediments; Lipids; Models, Biological; Phylogeny; Prokaryotic Cells; Symbiosis
PubMed: 31942073
DOI: 10.1038/s41586-019-1916-6 -
Transcription Oct 2020Increasingly sophisticated biochemical and genetic techniques are unraveling the regulatory factors and mechanisms that control gene expression in the Archaea. While... (Review)
Review
Increasingly sophisticated biochemical and genetic techniques are unraveling the regulatory factors and mechanisms that control gene expression in the Archaea. While some similarities in regulatory strategies are universal, archaeal-specific regulatory strategies are emerging to complement a complex patchwork of shared archaeal-bacterial and archaeal-eukaryotic regulatory mechanisms employed in the archaeal domain. The prokaryotic archaea encode core transcription components with homology to the eukaryotic transcription apparatus and also share a simplified eukaryotic-like initiation mechanism, but also deploy tactics common to bacterial systems to regulate promoter usage and influence elongation-termination decisions. We review the recently established complete archaeal transcription cycle, highlight recent findings of the archaeal transcription community and detail the expanding post-initiation regulation imposed on archaeal transcription.
Topics: Archaea; Transcription, Genetic
PubMed: 33112729
DOI: 10.1080/21541264.2020.1838865 -
Annual Review of Biochemistry Jun 2022Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two... (Review)
Review
Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.
Topics: Archaea; Bacteria; Bacterial Proteins; Iron; Phylogeny
PubMed: 35303791
DOI: 10.1146/annurev-biochem-040320-102858 -
Biotechnology Advances 2021Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are... (Review)
Review
Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.
Topics: Archaea; Bacteria; Biotechnology; Fungi; Industrial Microbiology; Polyhydroxyalkanoates
PubMed: 33271237
DOI: 10.1016/j.biotechadv.2020.107668 -
Annual Review of Microbiology Sep 2020It is now well recognized that the information processing machineries of archaea are far more closely related to those of eukaryotes than to those of their prokaryotic... (Review)
Review
It is now well recognized that the information processing machineries of archaea are far more closely related to those of eukaryotes than to those of their prokaryotic cousins, the bacteria. Extensive studies have been performed on the structure and function of the archaeal DNA replication origins, the proteins that define them, and the macromolecular assemblies that drive DNA unwinding and nascent strand synthesis. The results from various archaeal organisms across the archaeal domain of life show surprising levels of diversity at many levels-ranging from cell cycle organization to chromosome ploidy to replication mode and nature of the replicative polymerases. In the following, we describe recent advances in the field, highlighting conserved features and lineage-specific innovations.
Topics: Archaea; Archaeal Proteins; DNA Replication; DNA, Archaeal; Models, Molecular; Protein Binding
PubMed: 32503372
DOI: 10.1146/annurev-micro-020518-115443 -
FEMS Microbiology Letters Feb 2020
Topics: Archaea; Bacterial Physiological Phenomena; Host Microbial Interactions; Research; Symbiosis
PubMed: 32193538
DOI: 10.1093/femsle/fnz255 -
Biomolecules Apr 2020Since the pioneering work of Carl Woese, Archaea have fascinated biologists of almost all areas given their unique evolutionary status, wide distribution, high... (Review)
Review
Since the pioneering work of Carl Woese, Archaea have fascinated biologists of almost all areas given their unique evolutionary status, wide distribution, high diversity, and ability to grow in special environments. Archaea often thrive in extreme conditions such as high temperature, high/low pH, high salinity, and anoxic ecosystems. All of these are threats to the stability and proper functioning of biological molecules, especially proteins and nucleic acids. Post-translational modifications (PTMs), such as phosphorylation, methylation, acetylation, and glycosylation, are reportedly widespread in Archaea and represent a critical adaptive mechanism to extreme habitats. Here, we summarize our current understanding of the contributions of PTMs to aid in extremophile survival, with a particular focus on the maintenance of genome stability.
Topics: Archaea; Genomic Instability; Microbial Viability; Protein Processing, Post-Translational
PubMed: 32290118
DOI: 10.3390/biom10040584 -
Biomolecules Oct 2020Archaea often thrive in environmental extremes, enduring levels of heat, pressure, salinity, pH, and radiation that prove intolerable to most life. Many environmental... (Review)
Review
Archaea often thrive in environmental extremes, enduring levels of heat, pressure, salinity, pH, and radiation that prove intolerable to most life. Many environmental extremes raise the propensity for DNA damaging events and thus, impact DNA stability, placing greater reliance on molecular mechanisms that recognize DNA damage and initiate accurate repair. Archaea can presumably prosper in harsh and DNA-damaging environments in part due to robust DNA repair pathways but surprisingly, no DNA repair pathways unique to Archaea have been described. Here, we review the most recent advances in our understanding of archaeal DNA repair. We summarize DNA damage types and their consequences, their recognition by host enzymes, and how the collective activities of many DNA repair pathways maintain archaeal genomic integrity.
Topics: Archaea; DNA Damage; DNA Repair; DNA, Archaeal
PubMed: 33113933
DOI: 10.3390/biom10111472 -
Viruses Apr 2021This Special Issue celebrates viruses of microbes: those viruses that infect archaea, bacteria and microbial eukaryotes [...].
This Special Issue celebrates viruses of microbes: those viruses that infect archaea, bacteria and microbial eukaryotes [...].
Topics: Archaea; Bacteria; Eukaryota; Host-Pathogen Interactions; Microbiology; Virus Physiological Phenomena; Viruses
PubMed: 33946411
DOI: 10.3390/v13050802 -
Philosophical Transactions of the Royal... Nov 2019Cells are the building blocks of life, from single-celled microbes through to multi-cellular organisms. To understand a multitude of biological processes we need to...
Cells are the building blocks of life, from single-celled microbes through to multi-cellular organisms. To understand a multitude of biological processes we need to understand how cells behave, how they interact with each other and how they respond to their environment. The use of new methodologies is changing the way we study cells allowing us to study them on minute scales and in unprecedented detail. These same methods are allowing researchers to begin to sample the vast diversity of microbes that dominate natural environments. The aim of this special issue is to bring together research and perspectives on the application of new approaches to understand the biological properties of cells, including how they interact with other biological entities. This article is part of a discussion meeting issue 'Single cell ecology'.
Topics: Archaea; Bacterial Physiological Phenomena; Fungi; Single-Cell Analysis
PubMed: 31587644
DOI: 10.1098/rstb.2019.0076